Class to represent SNP annotation for a microarray

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Description

This class annotates a microarray SNP chip with data for each SNP including chromosome, id, position, strand, 'rs' id, allele 1, allele 2 for each SNP of a microarray chip, in either hg18, hg19 or hg38 (build 36/37/38) coordinates. This package makes extension use of this class of annotation object for the working microarray chip, e.g, default is ImmunoChip, and you can also load your own annotation if using a different chip. The class is basically a GRanges object, modified to always have columns for A1, A2 (alleles), rs.id, and a quality control flag. The default display is tidier than GRanges, it has nice coersion to and frame data.frame and subsetting by chromosome using [[n]] has been added, in addition to normal [i,j] indexing native to GRanges. Note that with this package the first time annotation is used it might be slow, but subsequent calls should be fast. METHODS "[[", show, print, length, dim, rownames, initialize build, chip, rs.id, A1, A2, QCcode, QCcode<-, QCpass, QCfail convTo36, convTo37, convTo38 COERCION can use 'as' to convert to and from: GRanges, RangedData, data.frame

Use the 'ChipInfo()' wrapper to construct ChipInfo objects from scratch

Usage

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## S4 method for signature 'ChipInfo'
initialize(.Object, ...)

Arguments

.Object

An object generated from the ChipInfo class prototype, see methods:initialize

...

Additional arguments to initialize. None recommended.

Fields

seqnames:

Object of class "Rle", containing chromosomes for each range, see GRanges.

ranges:

Object of class "IRanges", containing genomic start and end, see GRanges.

strand:

Object of class "Rle", containing plus or minus coding for forward or reverse strand, see GRanges.

seqinfo:

Object of class "Seqinfo", containing chromosome listing, see GRanges.

chip:

Name, class "character", containing user description of the chip, e.g, 'immunoChip'.

build:

Object of class "character", annotation version, e.g, hg18, hg19, hg38, etc.

elementMetaData:

Object of class "DataFrame", see GRanges, but with specific column names: A1, A2, QCcode and rs.id.

Author(s)

Nick Cooper

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